Genetic Basis for Metabolism of Methylated Sulfur Compounds in Methanosarcina Species

Abstract

Methanosarcina acetivorans uses a variety of methylated sulfur compounds as carbon and energy sources. Previous studies implicated the mtsD, mtsF, and mtsH genes in catabolism of dimethylsulfide, but the genes required for use of other methylsulfides have yet to be established. Here, we show that a four-gene locus, designated mtpCAP-msrH, is specifically required for growth on methylmercaptopropionate (MMPA). The mtpC, mtpA, and mtpP genes encode a putative corrinoid protein, a coenzyme M (CoM) methyltransferase, and a major facilitator superfamily (MFS) transporter, respectively, while msrH encodes a putative transcriptional regulator. Mutants lacking mtpC or mtpA display a severe growth defect in MMPA medium but are unimpaired during growth on other substrates. The mtpCAP genes comprise a transcriptional unit that is highly and specifically upregulated during growth on MMPA, whereas msrH is monocistronic and constitutively expressed. Mutants lacking msrH fail to transcribe mtpCAP and grow poorly in MMPA medium, consistent with the assignment of its product as a transcriptional activator. The mtpCAP-msrH locus is conserved in numerous marine methanogens, including eight Methanosarcina species that we showed are capable of growth on MMPA. Mutants lacking the mtsD, mtsF, and mtsH genes display a 30% reduction in growth yield when grown on MMPA, suggesting that these genes play an auxiliary role in MMPA catabolism. A quadruple ⌬mtpCAP ⌬mtsD ⌬mtsF ⌬mtsH mutant strain was incapable of growth on MMPA. Reanalysis of mtsD, mtsF, and mtsH mutants suggests that the preferred substrate for MtsD is dimethylsulfide, while the preferred substrate for MtsF is methanethiol. IMPORTANCEMethylated sulfur compounds play pivotal roles in the global sulfur and carbon cycles and contribute to global temperature homeostasis. Although the degradation of these molecules by aerobic bacteria has been well studied, relatively little is known regarding their fate in anaerobic ecosystems. In this study, we identify the genetic basis for metabolism of methylmercaptopropionate, dimethylsulfide, and methanethiol by strictly anaerobic methanogens of the genus Methanosarcina. These data will aid the development of predictive sulfur cycle models and enable molecular ecological approaches for the study of methylated sulfur metabolism in anaerobic ecosystems. M ethylated sulfur compounds (generically known as methylsulfides), including methylmercaptopropionate (MMPA), dimethylsulfide (DMS), and methanethiol (MeSH), are abundant in many ecosystems and play pivotal roles in the global sulfur and carbon cycles (1, 2). The predominate source of methylsulfides in marine systems is believed to be dimethylsulfoniopropionate (DMSP), a compatible solute whose synthesis by marine algae is estimated to account for 1 to 10% of global primary production (3). DMSP is degraded via two distinct microbial metabolic processes: the cleavage pathway and the demethylation pathway (1). The majority of DMSP (50 to 90%) is degraded via the demethylation pathway, pr...

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

“…Mts substantially vary in specificity to methylated thiol substrates, such as methanethiol (MeSH), dimethylsulfide (DMS), 3-methylmercaptopropionate (MMPA) and 3-mercaptopropionate (MPA; Tallant and Krzycki, 1997;Fu and Metcalf, 2015). Thus, accurate annotation of WSA2's methanogenic capacity necessitates systemic determination of the specific function of the two Mts homologs conserved among WSA2 genomes.…”

“…Although these groups have no experimentally studied representatives, their exclusive affiliation with methyldegrading methanogens suggests that these Mts homologs relate to methanogenic methyl metabolism. Family I is unlikely to support MeSH, DMS or MMPA metabolism as Methanosarcina acetivorans C2A does not express MA0847 during growth on these substrates (Bose et al, 2009;Fu and Metcalf, 2015). Thus, the metabolic function of family I-related WSA2 Mts-like protein (MtlA) is unclear.…”

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

“…Methanofuran is a component in the methyl-oxidation branch of methanogenesis playing a role in a key redox step inter-converting a formyl group and CO 2 and is required for all modes of methanogenic growth [37, 56]. Fifth, metabolic pathways for incorporating the methylated sulfur compound, methylmercaptopropionate, have been added/updated based on recent molecular biology studies [57]. Finally, several genes and a recently characterized reaction have been added to lipid biosythesis [58–60].…”

Thiol‐based redox sensing in the methyltransferase associated sensor kinase RdmS in Methanosarcina acetivorans

“…Here we present the first characterization of the multidomain SK RdmS as part of a multicomponent system regulating the expression of corrinoid/methyltransferase encoding genes in the methanogen M. acetivorans . These enzymes are thought to be required under circumstances when other substrates get scarce (Vepachedu and Ferry, ; Fu and Metcalf, ). Our data provide indications for direct interaction of RdmS with the three regulators MsrG/F/C but also give some mechanistic insight into signal perception and transduction in Methanosarcina .…”